from Bio.Align.Applications import MuscleCommandline

import os

muscle_exe = r"..\tools\muscle.exe"
in_file = r"..\data\human_2.txt"
out_file = r"..\data\human_3.txt"
muscle_cline = MuscleCommandline(muscle_exe, input=in_file, out=out_file)

stdout, stderr = muscle_cline()